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92  structures 446  species 2  interactions 3261  sequences 124  architectures

Family: MATH (PF00917)

Summary: MATH domain

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

MATH domain Provide feedback

This motif has been called the Meprin And TRAF-Homology (MATH) domain. This domain is hugely expanded in the nematode C. elegans [3].

Literature references

  1. Uren AG, Vaux DL; , Trends Biochem Sci 1996;21:244-245.: TRAF proteins and meprins share a conserved domain. PUBMED:8755243 EPMC:8755243

  2. McWhirter SM, Pullen SS, Holton JM, Crute JJ, Kehry MR, Alber T; , Proc Natl Acad Sci U S A 1999;96:8408-8413.: Crystallographic analysis of CD40 recognition and signaling by human TRAF2. PUBMED:10411888 EPMC:10411888

  3. Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D; , Science 1998;282:2022-2028.: Comparison of the complete protein sets of worm and yeast: orthology and divergence. PUBMED:9851918 EPMC:9851918


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002083

Although apparently functionally unrelated, intracellular TRAFs and extracellular meprins share a conserved region of about 180 residues, the meprin and TRAF homology (MATH) domain [PUBMED:12387856]. Meprins are mammalian tissue-specific metalloendopeptidases of the astacin family implicated in developmental, normal and pathological processes by hydrolysing a variety of proteins. Various growth factors, cytokines, and extracellular matrix proteins are substrates for meprins. They are composed of five structural domains: an N-terminal endopeptidase domain, a MAM domain (see PROSITEDOC), a MATH domain, an EGF-like domain (see PROSITEDOC) and a C-terminal transmembrane region. Meprin A and B form membrane bound homotetramer whereas homooligomers of meprin A are secreted. A proteolitic site adjacent to the MATH domain, only present in meprin A, allows the release of the protein from the membrane [PUBMED:7890660].

TRAF proteins were first isolated by their ability to interact with TNF receptors [PUBMED:8069916]. They promote cell survival by the activation of downstream protein kinases and, finally, transcription factors of the NF-kB and AP-1 family. The TRAF proteins are composed of 3 structural domains: a RING finger (see PROSITEDOC) in the N-terminal part of the protein, one to seven TRAF zinc fingers (see PROSITEDOC) in the middle and the MATH domain in the C-terminal part [PUBMED:12387856]. The MATH domain is necessary and sufficient for self-association and receptor interaction. From the structural analysis two consensus sequence recognised by the TRAF domain have been defined: a major one, [PSAT]x[QE]E and a minor one, PxQxxD [PUBMED:10518213].

The structure of the TRAF2 protein reveals a trimeric self-association of the MATH domain [PUBMED:10206649]. The domain forms a new, light-stranded antiparallel beta sandwich structure. A coiled-coil region adjacent to the MATH domain is also important for the trimerisation. The oligomerisation is essential for establishing appropriate connections to form signalling complexes with TNF receptor-1. The ligand binding surface of TRAF proteins is located in beta-strands 6 and 7 [PUBMED:10518213].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan TRAF (CL0389), which contains the following 3 members:

MATH Sina zf-TRAF

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(52)
Full
(3261)
Representative proteomes NCBI
(3079)
Meta
(7)
RP15
(726)
RP35
(1040)
RP55
(1659)
RP75
(2107)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(52)
Full
(3261)
Representative proteomes NCBI
(3079)
Meta
(7)
RP15
(726)
RP35
(1040)
RP55
(1659)
RP75
(2107)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(52)
Full
(3261)
Representative proteomes NCBI
(3079)
Meta
(7)
RP15
(726)
RP35
(1040)
RP55
(1659)
RP75
(2107)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_1602 (release 3.0)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 52
Number in full: 3261
Average length of the domain: 124.00 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 25.90 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.2 10.0
Trusted cut-off 21.2 10.0
Noise cut-off 21.1 9.9
Model length: 119
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

TRADD_N MATH

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the MATH domain has been found. There are 92 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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